Show simple item record

dc.contributor.authorHamblin, M.
dc.contributor.authorRabbi, Ismail Y
dc.identifier.citationHamblin, M. & Rabbi, I. Y. (2014). The Effects of Restriction-Enzyme Choice on Properties of Genotyping-by-Sequencing Libraries: A Study in Cassava (). Crop Science, 54(6), 2603-2608.
dc.description.abstractCompared with other reduced-representation sequencing methods, library construction for genotyping-by-sequencing (GBS) is simpler and less expensive. However, elimination of sizeselection steps results in libraries of more variable fragment size than with other reduced-representation methods, affecting several aspects of the data. To test the effect of restriction enzyme choice on library quality, we made GBS libraries with PstI (6-cutter), PstI/TaqI (4-cutter), or ApeKI (4.5-cutter) from the same set of DNAs from a cassava (Manihot esculenta Crantz) biparental population. Tag and single nucleotide polymorphism (SNP) counts were limited by the number of cut sites rather than by read number. Depth per locus was very skewed for the PstI library, such that most SNPs had low read depth but a subset had very high read depth. In contrast, the ApeKI and PstI/TaqI libraries had less variable distributions of read depth and yielded far more scorable SNPs. Our results suggest that 6-cutter enzymes may be most appropriate for genotyping a modest number of markers at a high multiplexing level, or for very large genomes, and perform better when used in a double digest with a 4-cutter enzyme.
dc.titleThe effects of restrictionenzyme choice on properties of genotypingbysequencing libraries: a study in cassava (Manihot esculenta)
dc.typeJournal Article
dc.description.versionPeer Review
cg.contributor.affiliationCornell University
cg.contributor.affiliationInternational Institute of Tropical Agriculture
cg.coverage.regionNorth America
cg.coverage.countryUnited States
cg.isijournalISI Journal
cg.authorship.typesCGIAR and advanced research institute
cg.journalCrop Science
cg.howpublishedFormally Published
cg.accessibilitystatusLimited Access

Files in this item


There are no files associated with this item.

This item appears in the following Collection(s)

Show simple item record